(→‎Q3: Is the synthetic biology community devoloping and operating awareness efforts?)

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<font color=red>09.08.06: please forgive the poor formatting of the references and links...these can be polished up into a single reference list and a uniform URL style once the text is refined. In the meantime, I'd welcome your feedback and have set up the associated talk page for this article for that purpose -NK</font color>

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The following series of practical questions and factual answers grew out of a well-intentioned notion that we might use the Q/A format to frame some issues relevant to the emerging field of synthetic biology and its societal implications. Our imagined audience is an intelligent, busy person interested in both technology and its risk/rewards. We welcome all feedback and impressions of this ongoing effort since we intend to refine, revise and update this work regularly. Post your thoughts on the associated discussion page or email them to nkuldell AT mit DOT edu and lmccray AT mit DOT edu.

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==Part 1: Defining the field and its capabilities==

==Part 1: Defining the field and its capabilities==

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===Question: How is synthetic biology different from existing, related fields like genetic engineering and metabolic engineering?===

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===Q1: How is synthetic biology different from existing, related fields like genetic engineering and metabolic engineering?===

In some ways, it's no different. People have been modifying genetic material for much of recorded history via breeding and genetic crosses. With the advent of recombinant DNA technology, more methodical combination of DNA segments became possible. Today, genomic data is available for many of the planet's organisms AND technologies exist to make the genetic material from scratch. These two technologies of sequencing and synthesis are key enabling technologies of synthetic biology.

In some ways, it's no different. People have been modifying genetic material for much of recorded history via breeding and genetic crosses. With the advent of recombinant DNA technology, more methodical combination of DNA segments became possible. Today, genomic data is available for many of the planet's organisms AND technologies exist to make the genetic material from scratch. These two technologies of sequencing and synthesis are key enabling technologies of synthetic biology.

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Traditionally, genetic engineering has been focused on making relatively small changes to biological systems: introducing a new gene into an organism, for instance. An illustrative example is that of improved insulin production through genetically engineering bacterial cells to express the human gene for that protein. By contrast, synthetic biology seeks to start from a "blank slate" and ask, what can we make? Thus, instead of perturbing existing systems and organisms, synthetic biologists attempt to construct new ones. Metabolic engineering can be thought of as a specialization of synthetic biology for the purpose of retooling cellular metabolism for human purposes. Synthetic biology also has applications in other areas like materials fabrication, energy production, information processing and more.[http://openwetware.org/index.php?title=User:NKuldell/Q/A_Read_more| Read more]

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Traditionally, genetic engineering has been focused on making relatively small changes to biological systems: introducing a new gene into an organism, for instance. An illustrative example is that of improved insulin production through genetically engineering bacterial cells to express the human gene for that protein. By contrast, synthetic biology seeks to start from a "blank slate" and ask, what can we make? Thus, instead of perturbing existing systems and organisms, synthetic biologists attempt to construct new ones. Metabolic engineering can be thought of as a specialization of synthetic biology for the purpose of retooling cellular metabolism for human purposes. Synthetic biology also has applications in other areas like materials fabrication, energy production, information processing and more.[[User:NKuldell/Q/A Read more| Read more]]

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===Question: Is there an expert review of the nature and potential benefits and risks of synthetic biology?===

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===Q2: Is there an expert review of the nature and potential benefits and risks of synthetic biology?===

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Here are some and more are still to come. <br>

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Some recent reviews are listed here. More are in the pipeline. <br>

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Reviews that focus on the technology itself are <br>

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<b>Reviews that focus on the technology itself are </b> <br>

*Sci Am Fab group

*Sci Am Fab group

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*Pam's G&D paper

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*Pam's G&D paper (coming soon?)

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*Voight,Keasling Nat Chem Biol. 2005 Nov;1(6):304-7

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*Voigt's TIBS (?) paper (coming soon?)

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*Paras Chopra and Akhil Kamma "Engineering Life through Synthetic Biology"

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*Voigt,Keasling Nat Chem Biol. 2005 Nov;1(6):304-7

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[http://www.bioinfo.de/isb/2006/06/0038/]

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*Paras Chopra and Akhil Kamma "Engineering Life through Synthetic Biology"[http://www.bioinfo.de/isb/2006/06/0038/]

===Question: What questions or applications are being addressed by synthetic biology that aren't being explored or built using other technologies?===

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===Q3: What questions or applications are being addressed by synthetic biology that aren't being explored or built using other technologies?===

Some synthetic biologists are combining genomic information and synthesis technologies to re-write the genetic code from living creatures. Just as computer programmers might want to re-write the code for your PC, these synthetic biologists annotate their changes to the genetic program of the system they are studying with the hope that each element of code may be more manipulable and human-readable. Successes on this frontier include refactoring T7 <cite>Chan-MSB-2005</cite>, two genomes in one cell <cite>Itaya-PNAS-2005</cite> and characterization of a minimal ''E. coli'' genome <cite>Posfai-Science-2006</cite>.

Some synthetic biologists are combining genomic information and synthesis technologies to re-write the genetic code from living creatures. Just as computer programmers might want to re-write the code for your PC, these synthetic biologists annotate their changes to the genetic program of the system they are studying with the hope that each element of code may be more manipulable and human-readable. Successes on this frontier include refactoring T7 <cite>Chan-MSB-2005</cite>, two genomes in one cell <cite>Itaya-PNAS-2005</cite> and characterization of a minimal ''E. coli'' genome <cite>Posfai-Science-2006</cite>.

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Finally, synthetic biology can provide a framework for discovery-driven biologists who might like to test their existing models by building them from the ground up. These efforts are reminiscent of those in chemical engineering, where the step-wise synthesis of a novel chemical compound is used to convincingly demonstrate a complete understanding of its chemistry. Along these lines, synthetic biologists have recently published a framework for characterizing interactions of novel synthetic protein dimerization domains <cite>Giesecke-MSB-2006</cite> and have applied this framework to determine dimerization specificity. Other efforts are focused on trying to construct chemical systems capable of evolution to study the fundamental properties of life <cite>Chen-JACS-2005</cite>.

Finally, synthetic biology can provide a framework for discovery-driven biologists who might like to test their existing models by building them from the ground up. These efforts are reminiscent of those in chemical engineering, where the step-wise synthesis of a novel chemical compound is used to convincingly demonstrate a complete understanding of its chemistry. Along these lines, synthetic biologists have recently published a framework for characterizing interactions of novel synthetic protein dimerization domains <cite>Giesecke-MSB-2006</cite> and have applied this framework to determine dimerization specificity. Other efforts are focused on trying to construct chemical systems capable of evolution to study the fundamental properties of life <cite>Chen-JACS-2005</cite>.

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===Q4: Why is biology so hard to engineer now?===

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===Question: Why is biology so hard to engineer now?===

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Engineers do not welcome uncertainty and unpredictable behavior but the biological world is full of these. Certainly the behavior of cells is guided by laws of the natural world (physics, inheritance etc.) but biology continues to surprise those who study it. And while surprises may be exciting for scientists, they constrain the activities of engineers who might like to reliably build with biological parts. Existing descriptions of basic cellular activities and genetic codes do not allow biological activities to be predictably combined in novel and re-useable ways.[[User:NKuldell/Q/A Read more| Read more]]

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<font color= blue><i>this seems most similar to runner up question "impediments to progress". this may or may not be relevant for Q/A series devoted to social implications of the field. worth considering further...-NK</i></font color>

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<font color="#ff0000"> I think it is important to understanding the "why" of syn bio - JB. </font>

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Biology has several features that are difficult or lacking in other engineering mediums including

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#Biological systems can manufacture materials and chemicals fast, on very small or very large scales, with minimal toxic byproducts and under gentle reaction conditions

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#Biological systems can evolve.

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#Most importantly, biological organisms can self-replicate.

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Genomic DNA sequences have been described as the programs that run biological machines, analogous to the computer programs that run PCs. Reading and interpreting DNA sequence (strings of A's,T's,G's and C's) is just as challenging as reading and interpreting binary code (strings of 0's and 1's). Imagine that someone has given you a printout of the binary code for the Microsoft Windows operating system (without telling you what it is) and asks you what the program does. It would be an incredibly difficult question to answer. Similarly, understanding DNA sequence information is also challenging. In fact, it is an even more difficult problem because at least Microsoft Windows was written by humans in a reasonably rational way. DNA sequences were written by evolution and so our ability to understand them is limited for now. Synthetic biology seeks to take the next step and actually "write new code" so to speak. Thus, given our lack of understanding of naturally occuring DNA code, it is not surprising that synthetic biology poses a challenge currently.

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Additionally, existing descriptions of basic cellular activities do not allow the activities to be predictably combined in novel and re-useable ways. Certainly the behavior of cells is guided by laws of the natural world (physics, inheritance etc.) but biology continues to surprise those who study it. And while surprises may be exciting for scientists, they constrain the activities of engineers who might like to reliably build with biological parts. Thus an important effort in synthetic biology aims to develop improved foundational technologies for reusing genetic elements. If successful, biological engineers might work with the confidence enjoyed by other engineering disciplines who don't, for example, need to build a bridge to know if it will fall down. Furthermore, once tamed, the features that make the engineering of biological systems difficult may yield novel systems capable of operations and behaviors not achievable by other engineering methods.

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The difficulties facing those who wish to engineer biology are concisely described by Endy <cite>Endy</cite> and Knight <cite>Knight-MSB-2005</cite>.

The difficulties facing those who wish to engineer biology are concisely described by Endy <cite>Endy</cite> and Knight <cite>Knight-MSB-2005</cite>.

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<biblio>

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#Knight-MSB-2005 pmid=16729055

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#Endy pmid=16306983

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</biblio>

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===Question: Some people may foresee a day when synthetic biology can build complex organisms from basic biological materials. Can simple viruses and primitive life forms already now be synthesized?===

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===Q5: Some people may foresee a day when synthetic biology can build complex organisms from basic biological materials. Can simple viruses and primitive life forms already now be synthesized?===

<font color="#ff0000"> N is correct, but I pesonally like this question since it gives a general idea of what the current state of the art is - does another question answer this more directly? - JB </font>

Viruses have been synthesized. Life forms, not yet. For example, in 2002 Cello, Paul and Wimmer reported the successful ''de novo'' synthesis of poliovirus <cite>Cello-Science-2002</cite>, assembling from raw chemicals an agent that could infect mice, although it required a whopping dose relative to the natural virus that leads to infection. The authors described their efforts as “fueled by a strong curiosity about the minute particles that we can view both as chemicals and as “living” entities.” Other examples of ''de novo'' synthesis of viruses are the phiX174 bacteriophage reported in 2003 <cite>Smith-PNAS-2003</cite> and human influenza in 2005<cite>Tumpey-Science-2003</cite>. Noteworthy are the speed with which these viruses could be made, a mere two weeks from raw chemicals to infectious bacteriophage in 2003, as well as the technology’s potential for synthesizing agents to harm rather than study nature <cite>vanAken-Nature-2006</cite>.

Viruses have been synthesized. Life forms, not yet. For example, in 2002 Cello, Paul and Wimmer reported the successful ''de novo'' synthesis of poliovirus <cite>Cello-Science-2002</cite>, assembling from raw chemicals an agent that could infect mice, although it required a whopping dose relative to the natural virus that leads to infection. The authors described their efforts as “fueled by a strong curiosity about the minute particles that we can view both as chemicals and as “living” entities.” Other examples of ''de novo'' synthesis of viruses are the phiX174 bacteriophage reported in 2003 <cite>Smith-PNAS-2003</cite> and human influenza in 2005<cite>Tumpey-Science-2003</cite>. Noteworthy are the speed with which these viruses could be made, a mere two weeks from raw chemicals to infectious bacteriophage in 2003, as well as the technology’s potential for synthesizing agents to harm rather than study nature <cite>vanAken-Nature-2006</cite>.

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Since viruses replicate only in living hosts, they are not themselves alive. A minimal life form would require self-replicating nucleic acids and a synthetic chassis in which to house them. A front-runner for the former is RNA with catalytic activity, including self-replication as described in 2001 <cite>Johnston-Science-2001</cite>. For the latter, lab built membrane vesicles to encapsulate RNA were described in 2005 <cite>Chen-JACS-2005</cite>, but these assemble only through directed manipulations of experimental conditions. Thus, it seems efforts to enclose self-replicating nucleic acids in some spontaneously assembling bubble are underway but, to date, only components of a lab-generated living cell have been reported (http://www.pbs.org/wgbh/nova/sciencenow/3214/01.html)

Since viruses replicate only in living hosts, they are not themselves alive. A minimal life form would require self-replicating nucleic acids and a synthetic chassis in which to house them. A front-runner for the former is RNA with catalytic activity, including self-replication as described in 2001 <cite>Johnston-Science-2001</cite>. For the latter, lab built membrane vesicles to encapsulate RNA were described in 2005 <cite>Chen-JACS-2005</cite>, but these assemble only through directed manipulations of experimental conditions. Thus, it seems efforts to enclose self-replicating nucleic acids in some spontaneously assembling bubble are underway but, to date, only components of a lab-generated living cell have been reported (http://www.pbs.org/wgbh/nova/sciencenow/3214/01.html)

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<biblio>

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===Q6: How quickly is the field moving towards its goals?===

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#Cello-Science-2002 pmid=12114528

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#Smith-PNAS-2003 pmid=14657399

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#Tumpey-Science-2003 pmid=16210530

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#vanAken-Nature-2006 pmid=16421546

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#Johnston-Science-2001 pmid=11358999

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#Chen-JACS-2005 pmid=16173749

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</biblio>

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===<font color="blue">Question: How quickly is the field moving towards its goals?===

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*<i>can this be answered factually?--NK </i></font color>

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<font color="#ff0000"> Maybe split into the following 2 questions or reword -

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===Question: What have been the major developments in SB? (f0r a timeline of past developments)</i>

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===Question: What are the major near and long term research objectives in SB? </i>

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Can you list major milestones/breakthroughs and current research here to give an idea of the pace of progress? - JB </font color>

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Events/dates suggested at 06.23.06 meeting for timeline:

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Relevant events that might be placed on a timeline:<i> dates, landmarks still needed</i>

One oft cited paper by Carlson <cite>Carlson</cite> looks at the improvements in the DNA sequencing and synthesis capacity in recent years. These two technologies are arguably the two key technologies that will enable the engineering of biological systems.

One oft cited paper by Carlson <cite>Carlson</cite> looks at the improvements in the DNA sequencing and synthesis capacity in recent years. These two technologies are arguably the two key technologies that will enable the engineering of biological systems. Related reference, not oft cited, is Zwick (2005) Technology: a genome sequencing center in every lab.

==Part 2: Defining the community==

==Part 2: Defining the community==

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===Question: What is the nature of the synthetic biology community?===

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===Q1: What is the nature of the synthetic biology community?===

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<font color= blue>alternatively phrased question: What is the nature of the SB community? thought this presumes an established community <font color="#ff0000"> not necessarily - could say "The community currently consists of several ad hoc groups, such as ___, ____, and ____." or something like that. It is just as important (to me) to communicate whether or not the community is established, and if so in what form as to describe who is doing the work. The level of community will indicate how well potential self regulation may work - if there are multiple groups that do not play well together it is unlikely that the community will be able to get them all to agree to and abide by a common standard for safety, security, ethics, etc. - JB </font color>

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*Approaches for answering:

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**estimates of numerical strength (both commercial and academic)

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**international distribution?

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**how are they funded?

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**Maybe we should also describe the typical backgrounds of those working in SB? Biologists, electrical engineers, computer scientists etc.

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<i>As an approach to answering this question we may want to search for meeting attendance numbers, SB departments, jobs that use SB in description, number of papers published with SB in title or abstract and where investigators are housed. As important as who is doing the work today is who will be doing the work tomorrow, so we may want to cite iGEM growth--NK

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Other ideas? </i>

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Presumably the SB 2.0 organizers could also give us data on the deparmental affiliations of the conference attendees?

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:At least in the case of SB1.0, we had a reasonably tight privacy policy that would preclude us from making this information available. Regardless, given the new nature of the field, I think that departmental affiliations might not tell us that much (just because an individual is interested in the field, doesn't mean their dept is).

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</font>

Like most emerging research fields, the synthetic biology community is loosely defined with no single unified voice. Members of the community span both industry and academia (although the latter likely outnumbers the former right now). Two conferences in the field have been held ([http://openwetware.org/wiki/Synthetic_Biology:Synthetic_Biology_1.0 Synthetic Biology 1.0] at MIT and [http://pbd.lbl.gov/sbconf/ Synthetic Biology 2.0] at UC Berkeley) each with approximately 300 participants. These two conferences constitute the most significant events that brought together the community.

Like most emerging research fields, the synthetic biology community is loosely defined with no single unified voice. Members of the community span both industry and academia (although the latter likely outnumbers the former right now). Two conferences in the field have been held ([http://openwetware.org/wiki/Synthetic_Biology:Synthetic_Biology_1.0 Synthetic Biology 1.0] at MIT and [http://pbd.lbl.gov/sbconf/ Synthetic Biology 2.0] at UC Berkeley) each with approximately 300 participants. These two conferences constitute the most significant events that brought together the community.

Yet in some ways the synthetic biology is quite organized given that it is in its early stages. For instance,

Yet in some ways the synthetic biology is quite organized given that it is in its early stages. For instance,

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#An NSF-funded effort called SynBERC was launched in August of 2006 [http://www.synberc.org/index.html]. SynBERC (Synthetic Biology Engineering Research Center) initiates a multi-institutional, collaborative effort to lay the foundations for engineering with biological substrates.

#A [http://syntheticbiology.org community website] exists that can be edited and revised by anyone in the field.

#A [http://syntheticbiology.org community website] exists that can be edited and revised by anyone in the field.

One measure of the growth of the field is the [http://parts.mit.edu/igem international Genetically Engineered Machines competition] or iGEM. iGEM is a competition in which teams of students from various universities compete to design, build and test an engineered biological system from standard biological parts. iGEM has its roots in a class held at MIT in January 2003 with ~20 students. It then expanded to an intercollegiate competition in 2004 between five U.S. schools. Currently, in 2006, there are ~39 universities and ~400 participants from across the world (see [http://openwetware.org/images/c/ce/IGEM2006worldmap.gif map]).

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===Question: Who speaks for the field? ===

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<font color= blue>There is no single spokesperson. This question presumes a defined and mature community and opens the opportunity for those of us answering to list ongoing activities to build community.</font>

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<font color="#ff0000"> It seems that even if the community is not well defined or mature that there will be a few people who come forth as spokepersons, whether they represent others or not. This question would give novices/interested parties an idea of who is making public statements and could also point them towards other sources of info/people who may not be publicly represented. This would be especially important if there are one or two outspoken scientists who do not represent the majority of research, but happen to get quoted for every newspaper article. It will also point reporters in the direction of whom to interview - JB </font color>

<font color= blue>organizational note on this section: though it's not an easy task, it would be ideal to balance benefits listed in this section (i.e., # of questions, importance of answers) with material offered in the "risk" section and with that provided in the "defining the field" section, to avoid leaving an anti-technology impression and to avoid looking narcissistic, respectively.

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</font color>

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===Question: What are the perceived benefits of synthetic biology?===

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Given Synthetic Biology's wide scope for engineering biological systems, the potential application space of synthetic biology is similarly enormous. Novel medical applications, environmental remediation, energy production and biomaterials synthesis may all be approachable through synthetic biology. In the future, cells may be quickly and predictably programmed to meet these and other discrete engineering goals. Synthetic biology may also benefit traditional biologists in their efforts to understand the natural world since these investigators may more easily test existing models of natural systems by building them from the ground up. Additionally, synthetic biology presents opportunities for synthetic chemists since cells may be considered self-replicating bags of interesting chemicals. Thus synthetic biology may enable the synthesis of novel chemical species under environmentally-gentle conditions.

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A more definitive answer to this question may arise as the community becomes better defined and mature. Activities to build community are ongoing (see Part 2, Question 1).

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===Question: Who is investing in this and what do they see as the pay-off?===

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==Part 3: Possible future benefits of synthetic biology==

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Currently much of the investment in the field is from the venture capital community into startup companies (e.g. [http://www.codondevices.com/ Codon Devices]). Codon Devices' goals are "in the short term, product opportunities include comprehensive sets of biological parts for large-scale research projects, engineered cells that produce novel pharmaceuticals, engineered protein biotherapeutics, and novel biosensor devices. In the longer term, the company's core technology is expected to enable improved vaccines, agricultural products, and biorefineries for the production of industrial chemicals and energy." [http://www.codondevices.com/] [http://www.syntheticgenomics.com/ Synthetic Genomics, Inc.], another startup by J. Craig Venter, believes "there are potentially limitless applications for synthetic biology/genomics, everything from energy to chemicals to pharmaceuticals. In the near-term, we think that synthetic genomics has applications in the areas of cleaner and more efficient energy production, specifically in the production of ethanol and hydrogen." [http://www.syntheticgenomics.com/about.htm]

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===Q1: What are the perceived benefits of synthetic biology?===

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Given synthetic biology's wide scope for engineering biological systems, the potential application space of synthetic biology is similarly enormous. Novel medical applications, environmental remediation, energy production and biomaterials synthesis may all be approachable through synthetic biology. In the future, cells may be quickly and predictably programmed to meet these and other discrete engineering goals. Synthetic biology may also benefit traditional biologists in their efforts to understand the natural world since these investigators may more easily test existing models of natural systems by building them from the ground up. Additionally, synthetic biology presents opportunities for synthetic chemists since cells may be considered self-replicating bags of interesting chemicals. Thus synthetic biology may enable the synthesis of novel chemical species under environmentally-gentle conditions.

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The European Union has also made research in the field of synthetic biology a priority with specific funding initiatives. [ftp://ftp.cordis.lu/pub/nest/docs/synthetic_biology.pdf pdf] The purpose of this funding is to stimulate science and technology research in the EU. The nonprofit [http://www.gatesfoundation.org/ Bill and Melinda Gates Foundation] has made significant investment in efforts by Jay Keasling and colleagues in synthesizing large quantities of the antimalarial artemisin . Their motivation is to solve critical world health problems. [http://www.gatesfoundation.org/globalhealth/pri_diseases/malaria/announcements/announce-041213.htm].

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===Q2: Who is investing in this and what do they see as the pay-off?===

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Thus the groups interested in synthetic biology span industry, government and nonprofit organizations. Each see a wealth of potential in the field but are interested in different application areas.

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The groups interested in synthetic biology span industry, government and nonprofit organizations. Each see a wealth of potential in the field but are interested in different application areas.

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===Question: Why would someone invest in this area as opposed to more traditional genetic engineering efforts?===

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Currently much of the investment in the field is from the venture capital community into startup companies (e.g. [http://www.codondevices.com/ Codon Devices]). Codon Devices' goals are "in the short term, product opportunities include comprehensive sets of biological parts for large-scale research projects, engineered cells that produce novel pharmaceuticals, engineered protein biotherapeutics, and novel biosensor devices. In the longer term, the company's core technology is expected to enable improved vaccines, agricultural products, and biorefineries for the production of industrial chemicals and energy." [http://www.codondevices.com/] [http://www.syntheticgenomics.com/ Synthetic Genomics, Inc.], another startup by J. Craig Venter, believes "there are potentially limitless applications for synthetic biology/genomics, everything from energy to chemicals to pharmaceuticals. In the near-term, we think that synthetic genomics has applications in the areas of cleaner and more efficient energy production, specifically in the production of ethanol and hydrogen." [http://www.syntheticgenomics.com/about.htm]

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<font color= blue><i>delete this Q/A?...it seems redundant with "benefits" question above, although there is a place for repetition in this kind of format--NK </i></font color>

The European Union has also made research in the field of synthetic biology a priority with specific funding initiatives. [ftp://ftp.cordis.lu/pub/nest/docs/synthetic_biology.pdf pdf] The purpose of this funding is to stimulate science and technology research in the EU. The nonprofit [http://www.gatesfoundation.org/ Bill and Melinda Gates Foundation] has made significant investment in efforts by Jay Keasling and colleagues in synthesizing large quantities of the antimalarial artemisin . Their motivation is to solve critical world health problems. [http://www.gatesfoundation.org/globalhealth/pri_diseases/malaria/announcements/announce-041213.htm].

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===Question: How can synthetic biology contribute to human health?===

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===Q3: How can synthetic biology contribute to human health?===

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<font color="#ff0000"> This could list research in these areas, or the potential for such research if basic hurdles are overcome. JB </font color>

A recent achievement in the field of synthetic biology for the purposes of human health is the recent report by Jay Keasling and colleagues at UC Berkeley and Amyris Biotechnologies regarding the microbial production of the antimalarial drug precursor artemisinic acid. This breakthrough is key to reducing the cost of this highly effective drug against malaria to a point where it is affordable to the 100 million people that die each year from malaria (<cite>Ro-Nature-2006</cite>, [http://www.amyrisbiotech.com/news_041206.html Amyris Biotechnologies press release]). Thus, synthetic biology offers the promise of synthesizing drugs cheaply and in an environmentally-friendly manner.

A recent achievement in the field of synthetic biology for the purposes of human health is the recent report by Jay Keasling and colleagues at UC Berkeley and Amyris Biotechnologies regarding the microbial production of the antimalarial drug precursor artemisinic acid. This breakthrough is key to reducing the cost of this highly effective drug against malaria to a point where it is affordable to the 100 million people that die each year from malaria (<cite>Ro-Nature-2006</cite>, [http://www.amyrisbiotech.com/news_041206.html Amyris Biotechnologies press release]). Thus, synthetic biology offers the promise of synthesizing drugs cheaply and in an environmentally-friendly manner.

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A longer term goal of synthetic biology is to potentially develop new kinds of therapeutics. For instance, Chris Voigt and colleagues at UCSF report the controlled invasion of cancer cells by engineered bacteria. These engineered bacteria are designed to sense environmental conditions associated with tumors and invade those cancer cells. One can imagine that such bacteria can eventually be engineered to selectively deliver drugs to and destroy the tumor itself. Such programmable behavior in living cells is a hallmark of synthetic biology.

A longer term goal of synthetic biology is to potentially develop new kinds of therapeutics. For instance, Chris Voigt and colleagues at UCSF report the controlled invasion of cancer cells by engineered bacteria. These engineered bacteria are designed to sense environmental conditions associated with tumors and invade those cancer cells. One can imagine that such bacteria can eventually be engineered to selectively deliver drugs to and destroy the tumor itself. Such programmable behavior in living cells is a hallmark of synthetic biology.

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<biblio>

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===Q4: What other classes of benefits are foreseen?===

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#Ro-Nature-2006 pmid=16612385

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#Voigt-JMB-2006 pmid=16330045

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</biblio>

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===Question: Is it hoped that SB will lead to new ways of “manufacturing” chemical entities that are now scarce or unavailable?===

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<font color="#ff0000"> Is insulin an example here?? JB </font color>

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===Question: What other classes of benefits are foreseen?===

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In addition to building on its early success in metabolic engineering of therapeutically relevant compounds, synthetic biology holds promise in other application areas.

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*note that these last three questions may be place holders for other benefits questions</font color>

===Q1: Does synthetic biology bring with it new risks not associated with existing, related fields?===

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The risks and rewards of synthetic biology are likely different from existing fields like genetic engineering and metabolic engineering. If synthetic biology is wildly successful then one can imagine a time when "garage inventors" could build something with biological materials. Genetic engineering, as it’s currently performed, requires substantial technical understanding of the project and access to specialized resources such as a laboratory and reagents. In the future, novel biological systems may be built with limited know-how, on a minimal budget and with no requirement for a specialized facility. It will be easy and cheap to make something not seen in nature, which means it could be done by folks who haven’t had the technology of genetic engineering at their disposal. Such democratization of biological engineering necessarily brings with it both the possibilities of a great number of useful applications as well as risks from accidental or intentional misuses.

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==Part 4: Possible future risks of synthetic biology==

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Understanding that synthetic biology brings with it new risks and rewards, one of the key missions of the nascent synthetic biological community is to forge a culture in which biological engineering happens responsibly. A full day of relevant discussion was programmed into the UC Berkeley hosted conference, [http://pbd.lbl.gov/sbconf/agenda.php Synthetic Biology 2.0, day 3]. Consequently, the Goldman School of Public Policy report [http://gspp.berkeley.edu/iths/UC%20White%20Paper.pdf PDF link] and a draft declaration from the conference [http://hdl.handle.net/1721.1/32982 pdf article] have been prepared. Additionally, some researchers within the community have self-organized to form a "synthetic society working group" [http://openwetware.org/wiki/Synthetic_Society], allowing scientists and engineers to engage with scholars expert in considering societal issues associated with emerging technologies, community leaders, and interested individuals. Finally, a report is anticipated from an ongoing project, sponsored by the Department of Energy and bio-era, that considers the impact of the genome synthesis and design [http://bio-era.net/research/add_research_17.html].

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NOTE: <i> <b> still under heavy construction </b> <font color= blue>I've brought all the questions of safeguards under this tent, since it might help balance the sky-is-falling feeling of this cluster. But perhaps the safeguard questions may be better placed under public perception or even community. Input? --NK</font color></i>

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===Question: Does synthetic biology bring with it new risks not associated with existing, related fields?===

The risks and rewards of synthetic biology are likely different from existing fields like genetic engineering and metabolic engineering. If synthetic biology is wildly successful then one can imagine a time when "garage inventors" could build something with biological materials. Genetic engineering, as it’s currently performed, requires substantial technical understanding of the project and access to specialized resources such as a laboratory and reagents. In the future, novel biological systems may be built with limited know-how, on a minimal budget and with no requirement for a specialized facility. It will be easy and cheap to make something not seen in nature, which means it could be done by folks who haven’t had the technology of genetic engineering at their disposal. Such democratization of biological engineering necessarily brings with it both the possibilities of a great number of useful applications as well as risks from accidental or intentional misuses. Understanding that Synthetic Biology brings with it new risks and rewards, one of the key missions of the nascent synthetic biological community is to forge a culture in which biological engineering happens responsibly.

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At the federal level, safety assurance is guided by

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*the <b> National Institutes of Health.</b> <br>The NIH has established guidelines for recombinant DNA [http://www4.od.nih.gov/oba/rac/guidelines_02/NIH_Guidelines_Apr_02.htm]. While they're called "guidelines", they're mandatory for any institution that receives funding from NIH.

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*the <b> Center for Disease Control.</b><br> The CDC has described "biosafety levels," [http://www.cdc.gov/OD/ohs/biosfty/bmbl4/bmbl4toc.htm] which establishes good lab practices for microbial agents. The Biosafety levels classify agents on a scale of one to four based on the risk the agents pose to human health, with correspondingly greater containment procedures considered good laboratory practice.

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*the <b>Occupational Safety and Health Administration. </b><br> OSHA has set standards for working with potentially infectious human materials [http://www.cdc.gov/OD/ohs/biosfty/bmbl4/bmbl4toc.htm].

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Additional regulations restrict import of biological materials [http://www.cdc.gov/od/eaipp/ ] and the use of "select agents" (agents with potential use in terrorism) [http://www.cdc.gov/od/sap/].

Safe laboratory practices are further defined and enforced at the state and local level. For example, waste disposal is regulated at the state level and individual research institutions are responsible for training its laboratory personel.

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<font color="#ff0000"> This is an important question - who has jurisdiction, and are they currently conducting any type of oversight?? A related question is - do they have the expertise and information to properly conduct oversight/regulation? JB </font color>

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</font color>

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** I will give this a go over the next few weeks starting with the premise that SB has safety/oversight methods no different from those that regulate more traditional recombinant research. I'll try to document what those are: what do funding agencies require? what do EHS/Biosafety regulations say? what RACs/protocols does a researcher need to file when undertaking research at an academic institution. Finally, as much as possible, I'll look into how these regulations differ for research in an industry setting. Other ideas/leads are welcome--Natalie

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*Info from Rhonda O'Keefe at MIT's EHS office:

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The NIH Guidelines for Recombinant DNA Research deal with rDNA. See this address: [http://www4.od.nih.gov/oba/rac/guidelines_02/NIH_Guidelines_Apr_02.htm] While they're called "guidelines", they're mandatory for any institution that receives funding from NIH. Another reference (not a regulation, but considered good practice) is called BMBL; it's published by the CDC and it spells out the biosafety levels. See this site: [http://www.cdc.gov/OD/ohs/biosfty/bmbl4/bmbl4toc.htm] . Also relevant is the OSHA Bloodborne Pathogen Standard for work with potentially infectious human materials; see this site: [http://www.cdc.gov/OD/ohs/biosfty/bmbl4/bmbl4toc.htm] . There are import regulations via the CDC [http://www.cdc.gov/od/eaipp/ ] as well as regulations on use of "select agents" [http://www.cdc.gov/od/sap/](agents with potential use in terrorism). Waste disposal is generally regulated on the state level.

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<font color = blue>

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<br> I can try to summarize the regulatory framework from these sources. -Natalie 07.27.06 </font color> <br>

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===Question: What are the existing barriers to the risk of potentially harmful synthetic biology products?===

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<i> thanks to Rhonda O'Keefe at MIT's EHS office for the links and descriptions </i>

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* answer should included mention of barriers in place to regulate research labs and commercial fabricators. Could also bring in surveillance ideas to monitor SB biohackers and any means of restricting products from overtly malicious agents (if there is evidence for this). As a correlary (or maybe as the lead line) can describe how community of openess and dialog (i.e. the “ethos” of current researchers) acts to anticipate and root out potential risk.

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<br>

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<i> would a "read more" section useful to summarize regulatory framework from these sources: what do funding agencies require? what do EHS/Biosafety regulations say? what RACs/protocols does a researcher need to file when undertaking research at an academic institution, how do these regulations differ for research in an industry setting. </i> <br>

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===Question: Are the safeguards established to regulate/oversee genetic engineering seen as working well?===

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===Q3: What are the existing barriers to the risk of potentially harmful synthetic biology products?===

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*this question can be rephrased to sound less opinion driven but seems important to include somehow as it allows us to include the fact that leadership in the research community helped setup safeguards that have successfully lowered risks from release of genetically altered organisms and accidental release of harmful ones. Can also include future SB plan for release of documentation if accidental release occurs.

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To date, release of synthetic biology products is regulated by laws that regulate more conventionally produced agents. For example, the US Food and Drug Administration [http://www.fda.gov/] is established to insure only safe and effective medicines are available to the consumer, and synthetic organisms that produce a drug (such as the yeast programmed by Jay Keasling's group to manufacture precursor of the anti-malarial drug artemisinin) are subject to the same scrutiny. Similarly, the US Environmental Protection Agency [http://www.epa.gov/] is charged with protecting both the environment and human health and any synthetic organism constructed for intentional release into the environment (it's worth noting that no synthetic biology products like this currently exist) would be similarly overseen and regulated.

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===Question: Is there evidence of interest in synthetic biology capabilities in the part of terrorists?===

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There may be additional and different risks associated with synthetic biology, if it successfully enables the rapid and facile design and construction of biological materials. Access to the required technology and reagents may be more widely distributed, thus construction of harmful products, intentionally or unintentionally, may be more possible. Consequently, the synthetic biology community is engaged in open and active dialogs to anticipate and address the impact of engineered organisms, and to enable only responsible efforts.

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* this question is posed from the view that those who are charged to limit the threat of terrorism may set their priorities based on hurdles that potential terrorists face in deploying destructive technologies. For example they may weigh the amount of scientific and technical know how required, the availability of expensive or controlled materials, danger to the miscreants themselves etc. Given that synthetic biology works to lower such barriers, it seems ripe for abuse but is there evidence that for such misappropriation of the technology. As part of the answer may want to explicitly describe what hurdles exist for the abuse of synthetic technologies by terrorists? as a start "DNA on demand significantly lowers barriers to potentially dangerous substances in the hands of miscreants. DNA synthesis companies have a record of synthesis orders but it’s not clear how or if that information would be shared. Most companies check sequence requests to look for ones that might encode dangerous substances and the companies can refuse to synthesize such DNA."

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===Question: Is biohacking possible?===

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*Existing approaches to answering this question include the idea that SB is sometimes presented as a special form of information processing technology…a program written for assembly of organisms or parts of organisms. This leads to the question: is it significantly more difficult for “biohackers” to cause mischief that those who wish for whatever reason to set loose the biological counterpart of a computer virus into the human environment?

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Another part of this answer has been that right now SB is incredibly hard. Very little works as predicted and there are only a few interchangeable parts to play with. But with time and success both these statements will be false and then hackers will have plenty to use for mischief. It might be best understood by thinking about computer operating systems and computer viruses. No computer viruses were written until lots of folks had their own computers and there were programs to attack and damage to be done. </font color>

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==Part 5: Social implications and public attitudes==

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<i>A "read more" answer could included mention of barriers in place to regulate research labs and commercial fabricators. Could also bring in surveillance ideas to monitor SB biohackers and any means of restricting products from overtly malicious agents (if there is evidence for this). </i>

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Note: <b> <i> still under heavy construction </i></b>

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===Q4: Is there evidence of interest in synthetic biology capabilities in the part of terrorists?===

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===<font color= blue>Question: Is the synthetic biology community seen as part of the genetic engineering community?===

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Facile DNA synthesis is a key enabling technology for synthetic biology, but DNA on demand significantly lowers barriers to potentially dangerous substances in the hands of miscreants. DNA synthesis companies have a record of synthesis orders but it’s not clear how or if that information would be shared. Most companies check sequence requests to look for ones that might encode dangerous substances. Companies can and have refused to synthesize such DNA. It is unclear, however, if the synthesis orders were placed by miscreants or by researchers with legitimate scientific interests. Thus, synthesis technology seems ripe for abuse but there is no evidence supporting or denying the misappropriation of the technology.

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*this is a question that tries to calibrate public confidence (Q15) by asking if misgivings or trust can be infered from those surrounding genetic engineering. As indicated in the lack of public controversy over the implementation of genetically engineering safeguards and the open release of GMO products, the public has some level of confidence in those who are doing that work. Is the SB community effectively part of the same community?

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<i>Still to add to answer: the view that those who are charged to limit the threat of terrorism may set their priorities based on hurdles that potential terrorists face in deploying destructive technologies. For example they may weigh the amount of scientific and technical know how required, the availability of expensive or controlled materials, danger to the miscreants themselves etc. Thus part of the answer may want to explicitly describe what hurdles exist for the abuse of synthetic technologies by terrorists? as a start </i>

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I'm a little unclear on the intent of this question, specifically the use of the work community rather than, for example, research agenda. Additionally, who is doing the seeing? Could it be rephrased as follows? - "Is synthetic biology distinct from genetic engineering in the minds of the public, administrators, and other relevant groups?"<br>

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===Q5: Is biohacking possible?===

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</font color>

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The answer to this question varies depending of the section of the public in question-

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Synthetic biology may offer a new toolkit for the longstanding and common human drive to manipulate nature. For example, what if in addition to the pears growing on a backyard pear tree, there could also be apples, two kinds, and perhaps a branch filled with quince. This unnatural tree could be made (indeed, has been made![http://forums2.gardenweb.com/forums/load/fruit/msg0815214723078.html?5]) through grafting of branches to heterologous but compatible trunks[http://www.make-digital.com/make/vol07/?pg=78]. What if the goal was to grow a pear tree with apple-flavored, quince-shaped fruits? Hybrid traits require more sophisticated methods, such as cross pollination, the method successfully used by Gregor Mendel to understand the laws of inheritance [http://www.visionlearning.com/library/module_viewer.php?mid=129&l=&c3=], or recombinant DNA technology, the method used to generate the "Flavr Savr" tomato [http://www.accessexcellence.org/RC/AB/BA/Flavr_Savr_Arrives.html]. The possibilities for biohacking expand considerably with synthetic biology. Fruit-flavored bacteria or yeast could be made. Indeed, a student-led synthetic biology team at MIT has produced bacteria that smell like bananas [http://openwetware.org/wiki/IGEM:MIT/2006/Blurb] and hope to import the circuitry to yeast to then bake some banana-bread without bananas...

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*For the average person in society with little or no formal training in Biology, given a 5min description of synthetic biology without specifically differentiating it from other fields, I believe it would be seen as indistinguishable from genetic engineering.

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*For the average biologist, given a 5min description of synthetic biology, I believe a distinction between the approach of the two fields would be seen, albeit a subtle one.

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*For the average funding agency or administrator, given the fact that the risks, benefits and applications are qualitatively similar for SB and GE, I believe they would be treated as one field.

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<font color= blue>

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===Question: What groups are closely following synthetic biology and its implications?===

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Deliberately mischievous biohacking is also possible and perhaps, eventually, easier, through synthetic biology. To date, the predictable design and fabrication of biological systems is limited. Very little works as predicted and there are only a few interchangeable biological parts to play with. But with time and success, both these statements will be false and then hackers will have plenty to use for mischief. It's hoped that better responses to mischief will also emerge, rapid construction of bioresponsive agents, perhaps, or self-destruct mechanisms and barcodes imbedded into all the biological parts to guard against their mis-use.

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* Question is looking for an SB "watchdog," and there is none (at least none dedicated to SB). Public perceptions are sometimes affected by the knowledge that entities exist that focus on palpable risks, playing a “watchdog” role. If there are no public or private groups that appear to be applying vigilance against or address events involving man-made organisms, are there other assurances to offer?

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===Question: Are there relevant lessons to be learned from existing, related technologies?===

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*answer could detail perceived risks with other S/T disciplines that have confronted and managed public risks: nuclear safety, hazardous chemical, GE, cryptography. Can ask if these provide suggestions as to the future role of the SB community. Can also mention lessons that have already been translated into action.

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===Question: Is the synthetic biology community devoloping and operating awareness efforts?===

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*this question was originally posed to probe public awareness efforts. Premise is: for some potentially risky technologies, professional organizations themselves develop and operate awareness efforts and training aids to reduce public and worker risk and asks if the SB community already doing this. This answer might offer nice place to talk about curriculum/education efforts underway.

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</font color>

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<i> "read more" section might further explore "biohacking" as biological counterpart of a computer virus in the human environment </i>

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==Part 5: Social implications and public attitudes==

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===Q1: Is synthetic biology distinct from genetic engineering in the minds of the public, administrators, and other relevant groups?===

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The answer to this question is likely to vary depending of the section of the public in question. An interesting experiment would be to provide a five minute description of synthetic biology, without specifically differentiating it from other fields, and then ask how synthetic biology compares to genetic engineering. It seems likely that

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*For the average person in society with little or no formal training in biology, synthetic biology would be seen as indistinguishable from genetic engineering.

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*For the average biologist, a distinct approaches of the two fields would be seen, but perhaps considered a subtle one.

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*For the average funding agency or administrator, given the fact that the risks, benefits and applications are qualitatively similar, synthetic biology and genetic engineering might be viewed as one field.

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==Runner-up questions==

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===Q2: What groups are closely following synthetic biology and its implications?===

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===Part 1: defining the field and its capabilities===

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* Origins? How and when did SB emerge as a distinct field? From what precursors?

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* Self-Selection Rules? Why did SB researchers decide to enter this new field? What background characteristics do they share?

* Extinction Risk? Is it possible that SB will lead to the eventual replacement of natural species by artificial ones?

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* Process Risks? In addition to the risk of effects of new synthesized organisms – and components of organisms – is there a risk of changed scientific publishing practices, of our concept of what “life” is, of reifying the analogy between computer codes and biological code? Other?

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===Part 5: social implications, public attitudes===

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* Applications Gatekeepers? Who are the likely gatekeepers for the SB applications that emerge? Will profit potential prove to be the primary factor in deciding what applications are pursued? What intellectual-property considerations will influence what applications are pursued?

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*Open Software and Risk? What is the relationship between the possibility of SB-hacking and the movement toward free and open software in the SB community?

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* Worst-Case Planning? In the event that we learn of an adverse event involving a potentially hazardous manmade organism, are there those who are ready and able to undertake effective remedial action? Has the remedial program been tested and validated by simulated game-playing or other proven techniques? [If Ans= “none,” weave this Q into others?]

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**editorialized answer: I don’t know if any “worse case scenarios” and “best case responses” have been detailed. If the response to recent natural disasters and public health threats is any guide, then we’d be foolish to expect government agencies to protect our well being through such crises. --NK

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==Cutting Room Floor?==

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Emerging technologies, including synthetic biology and its implications, are being followed and reported in the academic press. For example the European Molecular Biology Organization ("EMBO") published a special issue of EMBO Reports dedicated to science and security issues [http://www.nature.com/embor/journal/v7/n1s/index.html]. The lay press has also taken an interest in this area, for example the recent issue of MAKE magazine (volume 7) dedicated to backyard biology and garage biotechnology. Finally, many social organizations, including "watchdog" groups seeking vigilant oversight of the work and inclusion in the regulatory dialog, are interested and following development of this field. See for example their open letter to the synthetic biology community: [[Image:Macintosh HD-Users-nkuldell-Desktop-OpenLetter061805.pdf]].

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===Question:The Safety Record for GE? Some number of genetically engineered organisms have by now been unintentionally introduced into commerce and the environment. Have there been unanticipated adverse health or ecological impacts from these introductions? Who is monitoring this area? ===

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===Q3: Is the synthetic biology community developing and operating awareness efforts?===

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Genetically modified crops have upset and worried many folks, in no small part because there seems to be no one who is monitoring or controlling the release of such agents. Reaction to genetically modified pets (like GFP-fish or allergy-friendly cats) has been small by comparison.

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===Question: Intramural Risk Identification? What do those working closely on SB see as the plausible way that SB might be misused? Have they taken steps to see that policy or other counter measures are taken to minimize such possibilities? ===

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Educational information and curriculum is being written by members of the synthetic biology community. These include:

*[[http://syntheticbiology.org/| SyntheticBiology.org]] is an open forum for collecting and discussing relevant topics in synthetic biology

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*a student competition in synthetic biology called [http://parts.mit.edu/wiki/index.php/Main_Page iGEM]], which stands for International Genetically Engineered Machines, attracts and educates new students in synthetic biology as well as populates [[http://parts.mit.edu/registry/index.php/Main_Page the Registry of Standard Biological Parts]]

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*methodical and discipline-specific curriculum, for example [[http://openwetware.org/wiki/Keasling%3A_Synthetic_Biology_Class at UC Berkeley]] and [[http://openwetware.org/wiki/BE.109%3ASystems_engineering at MIT]], is being developed to train university students in synthetic biology

Latest revision as of 13:02, 11 September 2006

09.08.06: please forgive the poor formatting of the references and links...these can be polished up into a single reference list and a uniform URL style once the text is refined. In the meantime, I'd welcome your feedback and have set up the associated talk page for this article for that purpose -NK

The following series of practical questions and factual answers grew out of a well-intentioned notion that we might use the Q/A format to frame some issues relevant to the emerging field of synthetic biology and its societal implications. Our imagined audience is an intelligent, busy person interested in both technology and its risk/rewards. We welcome all feedback and impressions of this ongoing effort since we intend to refine, revise and update this work regularly. Post your thoughts on the associated discussion page or email them to nkuldell AT mit DOT edu and lmccray AT mit DOT edu.

Part 1: Defining the field and its capabilities

Q1: How is synthetic biology different from existing, related fields like genetic engineering and metabolic engineering?

In some ways, it's no different. People have been modifying genetic material for much of recorded history via breeding and genetic crosses. With the advent of recombinant DNA technology, more methodical combination of DNA segments became possible. Today, genomic data is available for many of the planet's organisms AND technologies exist to make the genetic material from scratch. These two technologies of sequencing and synthesis are key enabling technologies of synthetic biology.
Traditionally, genetic engineering has been focused on making relatively small changes to biological systems: introducing a new gene into an organism, for instance. An illustrative example is that of improved insulin production through genetically engineering bacterial cells to express the human gene for that protein. By contrast, synthetic biology seeks to start from a "blank slate" and ask, what can we make? Thus, instead of perturbing existing systems and organisms, synthetic biologists attempt to construct new ones. Metabolic engineering can be thought of as a specialization of synthetic biology for the purpose of retooling cellular metabolism for human purposes. Synthetic biology also has applications in other areas like materials fabrication, energy production, information processing and more. Read more

Q2: Is there an expert review of the nature and potential benefits and risks of synthetic biology?

Some recent reviews are listed here. More are in the pipeline. Reviews that focus on the technology itself are

Sci Am Fab group

Pam's G&D paper (coming soon?)

Voigt's TIBS (?) paper (coming soon?)

Voigt,Keasling Nat Chem Biol. 2005 Nov;1(6):304-7

Paras Chopra and Akhil Kamma "Engineering Life through Synthetic Biology"[1]

Custom-Made Microbes, at Your Service by A Pollack NYT Science section January 17, 2006 link

Q3: What questions or applications are being addressed by synthetic biology that aren't being explored or built using other technologies?

Some synthetic biologists are combining genomic information and synthesis technologies to re-write the genetic code from living creatures. Just as computer programmers might want to re-write the code for your PC, these synthetic biologists annotate their changes to the genetic program of the system they are studying with the hope that each element of code may be more manipulable and human-readable. Successes on this frontier include refactoring T7 [1], two genomes in one cell [2] and characterization of a minimal E. coli genome [3].
Other successful efforts in synthetic biology involve metabolic engineering of simple organisms like bacteria or yeast, enabling future production of therapeutics, such as tumor-seeking bacteria [3] or compounds whose natural reservoirs are in short supply. A recent noteable success in this effort is production of artemisinic acid in yeast [4], an achievement that may allow cheap and clean production of this precursor for an antimalarial drug.
Finally, synthetic biology can provide a framework for discovery-driven biologists who might like to test their existing models by building them from the ground up. These efforts are reminiscent of those in chemical engineering, where the step-wise synthesis of a novel chemical compound is used to convincingly demonstrate a complete understanding of its chemistry. Along these lines, synthetic biologists have recently published a framework for characterizing interactions of novel synthetic protein dimerization domains [5] and have applied this framework to determine dimerization specificity. Other efforts are focused on trying to construct chemical systems capable of evolution to study the fundamental properties of life [6].

Q4: Why is biology so hard to engineer now?

Engineers do not welcome uncertainty and unpredictable behavior but the biological world is full of these. Certainly the behavior of cells is guided by laws of the natural world (physics, inheritance etc.) but biology continues to surprise those who study it. And while surprises may be exciting for scientists, they constrain the activities of engineers who might like to reliably build with biological parts. Existing descriptions of basic cellular activities and genetic codes do not allow biological activities to be predictably combined in novel and re-useable ways. Read more

The difficulties facing those who wish to engineer biology are concisely described by Endy [7] and Knight [8].

Q5: Some people may foresee a day when synthetic biology can build complex organisms from basic biological materials. Can simple viruses and primitive life forms already now be synthesized?

Viruses have been synthesized. Life forms, not yet. For example, in 2002 Cello, Paul and Wimmer reported the successful de novo synthesis of poliovirus [9], assembling from raw chemicals an agent that could infect mice, although it required a whopping dose relative to the natural virus that leads to infection. The authors described their efforts as “fueled by a strong curiosity about the minute particles that we can view both as chemicals and as “living” entities.” Other examples of de novo synthesis of viruses are the phiX174 bacteriophage reported in 2003 [10] and human influenza in 2005[11]. Noteworthy are the speed with which these viruses could be made, a mere two weeks from raw chemicals to infectious bacteriophage in 2003, as well as the technology’s potential for synthesizing agents to harm rather than study nature [12].

Since viruses replicate only in living hosts, they are not themselves alive. A minimal life form would require self-replicating nucleic acids and a synthetic chassis in which to house them. A front-runner for the former is RNA with catalytic activity, including self-replication as described in 2001 [13]. For the latter, lab built membrane vesicles to encapsulate RNA were described in 2005 [6], but these assemble only through directed manipulations of experimental conditions. Thus, it seems efforts to enclose self-replicating nucleic acids in some spontaneously assembling bubble are underway but, to date, only components of a lab-generated living cell have been reported (http://www.pbs.org/wgbh/nova/sciencenow/3214/01.html)

Q6: How quickly is the field moving towards its goals?

Relevant events that might be placed on a timeline: dates, landmarks still needed

One oft cited paper by Carlson [14] looks at the improvements in the DNA sequencing and synthesis capacity in recent years. These two technologies are arguably the two key technologies that will enable the engineering of biological systems. Related reference, not oft cited, is Zwick (2005) Technology: a genome sequencing center in every lab.

Part 2: Defining the community

Q1: What is the nature of the synthetic biology community?

Like most emerging research fields, the synthetic biology community is loosely defined with no single unified voice. Members of the community span both industry and academia (although the latter likely outnumbers the former right now). Two conferences in the field have been held (Synthetic Biology 1.0 at MIT and Synthetic Biology 2.0 at UC Berkeley) each with approximately 300 participants. These two conferences constitute the most significant events that brought together the community.

Yet in some ways the synthetic biology is quite organized given that it is in its early stages. For instance,

An NSF-funded effort called SynBERC was launched in August of 2006 [4]. SynBERC (Synthetic Biology Engineering Research Center) initiates a multi-institutional, collaborative effort to lay the foundations for engineering with biological substrates.

A more definitive answer to this question may arise as the community becomes better defined and mature. Activities to build community are ongoing (see Part 2, Question 1).

Part 3: Possible future benefits of synthetic biology

Q1: What are the perceived benefits of synthetic biology?

Given synthetic biology's wide scope for engineering biological systems, the potential application space of synthetic biology is similarly enormous. Novel medical applications, environmental remediation, energy production and biomaterials synthesis may all be approachable through synthetic biology. In the future, cells may be quickly and predictably programmed to meet these and other discrete engineering goals. Synthetic biology may also benefit traditional biologists in their efforts to understand the natural world since these investigators may more easily test existing models of natural systems by building them from the ground up. Additionally, synthetic biology presents opportunities for synthetic chemists since cells may be considered self-replicating bags of interesting chemicals. Thus synthetic biology may enable the synthesis of novel chemical species under environmentally-gentle conditions.

Q2: Who is investing in this and what do they see as the pay-off?

The groups interested in synthetic biology span industry, government and nonprofit organizations. Each see a wealth of potential in the field but are interested in different application areas.

Currently much of the investment in the field is from the venture capital community into startup companies (e.g. Codon Devices). Codon Devices' goals are "in the short term, product opportunities include comprehensive sets of biological parts for large-scale research projects, engineered cells that produce novel pharmaceuticals, engineered protein biotherapeutics, and novel biosensor devices. In the longer term, the company's core technology is expected to enable improved vaccines, agricultural products, and biorefineries for the production of industrial chemicals and energy." [5]Synthetic Genomics, Inc., another startup by J. Craig Venter, believes "there are potentially limitless applications for synthetic biology/genomics, everything from energy to chemicals to pharmaceuticals. In the near-term, we think that synthetic genomics has applications in the areas of cleaner and more efficient energy production, specifically in the production of ethanol and hydrogen." [6]

The European Union has also made research in the field of synthetic biology a priority with specific funding initiatives. pdf The purpose of this funding is to stimulate science and technology research in the EU. The nonprofit Bill and Melinda Gates Foundation has made significant investment in efforts by Jay Keasling and colleagues in synthesizing large quantities of the antimalarial artemisin . Their motivation is to solve critical world health problems. [7].

Q3: How can synthetic biology contribute to human health?

A recent achievement in the field of synthetic biology for the purposes of human health is the recent report by Jay Keasling and colleagues at UC Berkeley and Amyris Biotechnologies regarding the microbial production of the antimalarial drug precursor artemisinic acid. This breakthrough is key to reducing the cost of this highly effective drug against malaria to a point where it is affordable to the 100 million people that die each year from malaria ([4], Amyris Biotechnologies press release). Thus, synthetic biology offers the promise of synthesizing drugs cheaply and in an environmentally-friendly manner.

A longer term goal of synthetic biology is to potentially develop new kinds of therapeutics. For instance, Chris Voigt and colleagues at UCSF report the controlled invasion of cancer cells by engineered bacteria. These engineered bacteria are designed to sense environmental conditions associated with tumors and invade those cancer cells. One can imagine that such bacteria can eventually be engineered to selectively deliver drugs to and destroy the tumor itself. Such programmable behavior in living cells is a hallmark of synthetic biology.

Q4: What other classes of benefits are foreseen?

In addition to building on its early success in metabolic engineering of therapeutically relevant compounds, synthetic biology holds promise in other application areas.
These still futuristic visions include:

clean chemistry. Facile biosynthesis of compounds that now require harsh conditions for fabrication.

information processing. Not bacteria as supercomputers, but rather implementing computing power where none currently exists.

ideally will have link to "Read more" for each item on list

Part 4: Possible future risks and safeguards for synthetic biology

Q1: Does synthetic biology bring with it new risks not associated with existing, related fields?

The risks and rewards of synthetic biology are likely different from existing fields like genetic engineering and metabolic engineering. If synthetic biology is wildly successful then one can imagine a time when "garage inventors" could build something with biological materials. Genetic engineering, as it’s currently performed, requires substantial technical understanding of the project and access to specialized resources such as a laboratory and reagents. In the future, novel biological systems may be built with limited know-how, on a minimal budget and with no requirement for a specialized facility. It will be easy and cheap to make something not seen in nature, which means it could be done by folks who haven’t had the technology of genetic engineering at their disposal. Such democratization of biological engineering necessarily brings with it both the possibilities of a great number of useful applications as well as risks from accidental or intentional misuses.

Understanding that synthetic biology brings with it new risks and rewards, one of the key missions of the nascent synthetic biological community is to forge a culture in which biological engineering happens responsibly. A full day of relevant discussion was programmed into the UC Berkeley hosted conference, Synthetic Biology 2.0, day 3. Consequently, the Goldman School of Public Policy report PDF link and a draft declaration from the conference pdf article have been prepared. Additionally, some researchers within the community have self-organized to form a "synthetic society working group" [8], allowing scientists and engineers to engage with scholars expert in considering societal issues associated with emerging technologies, community leaders, and interested individuals. Finally, a report is anticipated from an ongoing project, sponsored by the Department of Energy and bio-era, that considers the impact of the genome synthesis and design [9].

Synthetic biology is regulated by the safety and oversight programs that regulate more traditional recombinant and microbial research.

At the federal level, safety assurance is guided by

the National Institutes of Health.The NIH has established guidelines for recombinant DNA [10]. While they're called "guidelines", they're mandatory for any institution that receives funding from NIH.

the Center for Disease Control. The CDC has described "biosafety levels," [11] which establishes good lab practices for microbial agents. The Biosafety levels classify agents on a scale of one to four based on the risk the agents pose to human health, with correspondingly greater containment procedures considered good laboratory practice.

the Occupational Safety and Health Administration. OSHA has set standards for working with potentially infectious human materials [12].

Additional regulations restrict import of biological materials [13] and the use of "select agents" (agents with potential use in terrorism) [14].

Safe laboratory practices are further defined and enforced at the state and local level. For example, waste disposal is regulated at the state level and individual research institutions are responsible for training its laboratory personel.

thanks to Rhonda O'Keefe at MIT's EHS office for the links and descriptions would a "read more" section useful to summarize regulatory framework from these sources: what do funding agencies require? what do EHS/Biosafety regulations say? what RACs/protocols does a researcher need to file when undertaking research at an academic institution, how do these regulations differ for research in an industry setting.

Q3: What are the existing barriers to the risk of potentially harmful synthetic biology products?

To date, release of synthetic biology products is regulated by laws that regulate more conventionally produced agents. For example, the US Food and Drug Administration [15] is established to insure only safe and effective medicines are available to the consumer, and synthetic organisms that produce a drug (such as the yeast programmed by Jay Keasling's group to manufacture precursor of the anti-malarial drug artemisinin) are subject to the same scrutiny. Similarly, the US Environmental Protection Agency [16] is charged with protecting both the environment and human health and any synthetic organism constructed for intentional release into the environment (it's worth noting that no synthetic biology products like this currently exist) would be similarly overseen and regulated.

There may be additional and different risks associated with synthetic biology, if it successfully enables the rapid and facile design and construction of biological materials. Access to the required technology and reagents may be more widely distributed, thus construction of harmful products, intentionally or unintentionally, may be more possible. Consequently, the synthetic biology community is engaged in open and active dialogs to anticipate and address the impact of engineered organisms, and to enable only responsible efforts.

A "read more" answer could included mention of barriers in place to regulate research labs and commercial fabricators. Could also bring in surveillance ideas to monitor SB biohackers and any means of restricting products from overtly malicious agents (if there is evidence for this).

Q4: Is there evidence of interest in synthetic biology capabilities in the part of terrorists?

Facile DNA synthesis is a key enabling technology for synthetic biology, but DNA on demand significantly lowers barriers to potentially dangerous substances in the hands of miscreants. DNA synthesis companies have a record of synthesis orders but it’s not clear how or if that information would be shared. Most companies check sequence requests to look for ones that might encode dangerous substances. Companies can and have refused to synthesize such DNA. It is unclear, however, if the synthesis orders were placed by miscreants or by researchers with legitimate scientific interests. Thus, synthesis technology seems ripe for abuse but there is no evidence supporting or denying the misappropriation of the technology.

Still to add to answer: the view that those who are charged to limit the threat of terrorism may set their priorities based on hurdles that potential terrorists face in deploying destructive technologies. For example they may weigh the amount of scientific and technical know how required, the availability of expensive or controlled materials, danger to the miscreants themselves etc. Thus part of the answer may want to explicitly describe what hurdles exist for the abuse of synthetic technologies by terrorists? as a start

Q5: Is biohacking possible?

Synthetic biology may offer a new toolkit for the longstanding and common human drive to manipulate nature. For example, what if in addition to the pears growing on a backyard pear tree, there could also be apples, two kinds, and perhaps a branch filled with quince. This unnatural tree could be made (indeed, has been made![17]) through grafting of branches to heterologous but compatible trunks[18]. What if the goal was to grow a pear tree with apple-flavored, quince-shaped fruits? Hybrid traits require more sophisticated methods, such as cross pollination, the method successfully used by Gregor Mendel to understand the laws of inheritance [19], or recombinant DNA technology, the method used to generate the "Flavr Savr" tomato [20]. The possibilities for biohacking expand considerably with synthetic biology. Fruit-flavored bacteria or yeast could be made. Indeed, a student-led synthetic biology team at MIT has produced bacteria that smell like bananas [21] and hope to import the circuitry to yeast to then bake some banana-bread without bananas...

Deliberately mischievous biohacking is also possible and perhaps, eventually, easier, through synthetic biology. To date, the predictable design and fabrication of biological systems is limited. Very little works as predicted and there are only a few interchangeable biological parts to play with. But with time and success, both these statements will be false and then hackers will have plenty to use for mischief. It's hoped that better responses to mischief will also emerge, rapid construction of bioresponsive agents, perhaps, or self-destruct mechanisms and barcodes imbedded into all the biological parts to guard against their mis-use.

"read more" section might further explore "biohacking" as biological counterpart of a computer virus in the human environment

Part 5: Social implications and public attitudes

Q1: Is synthetic biology distinct from genetic engineering in the minds of the public, administrators, and other relevant groups?

The answer to this question is likely to vary depending of the section of the public in question. An interesting experiment would be to provide a five minute description of synthetic biology, without specifically differentiating it from other fields, and then ask how synthetic biology compares to genetic engineering. It seems likely that

For the average person in society with little or no formal training in biology, synthetic biology would be seen as indistinguishable from genetic engineering.

For the average biologist, a distinct approaches of the two fields would be seen, but perhaps considered a subtle one.

For the average funding agency or administrator, given the fact that the risks, benefits and applications are qualitatively similar, synthetic biology and genetic engineering might be viewed as one field.

Q2: What groups are closely following synthetic biology and its implications?

Emerging technologies, including synthetic biology and its implications, are being followed and reported in the academic press. For example the European Molecular Biology Organization ("EMBO") published a special issue of EMBO Reports dedicated to science and security issues [22]. The lay press has also taken an interest in this area, for example the recent issue of MAKE magazine (volume 7) dedicated to backyard biology and garage biotechnology. Finally, many social organizations, including "watchdog" groups seeking vigilant oversight of the work and inclusion in the regulatory dialog, are interested and following development of this field. See for example their open letter to the synthetic biology community: File:Macintosh HD-Users-nkuldell-Desktop-OpenLetter061805.pdf.

Q3: Is the synthetic biology community developing and operating awareness efforts?

Educational information and curriculum is being written by members of the synthetic biology community. These include:

[SyntheticBiology.org] is an open forum for collecting and discussing relevant topics in synthetic biology

a student competition in synthetic biology called iGEM], which stands for International Genetically Engineered Machines, attracts and educates new students in synthetic biology as well as populates [the Registry of Standard Biological Parts]

methodical and discipline-specific curriculum, for example [at UC Berkeley] and [at MIT], is being developed to train university students in synthetic biology